At the 10x Genomics Global Cell Therapy Virtual Symposium, held February 8–12, leading cancer immunotherapy researchers discussed the challenges and promises of T-cell therapy. In this post, we highlight key points of the panel roundtable, including discussion points around four key themes: characterizing the leukapheresis and infusion product, the evolution of the cell product in vivo, mechanisms of resistance, and next-generation cell therapies.
We’re thrilled with the success of the 10x Genomics Global Cell Therapy Virtual Symposium, held February 8–12. At this virtual webinar series designed to bring the global community of cancer immunotherapy researchers together, leading scientists converged for a week of engaging presentations as well as a live discussion panel.
During the panel, speakers discussed several key topics around single cell resolution and how it can help uncover molecular insights into cell therapeutic efficacy and toxicity, which continue to be critical research areas. In this post, we’ll recap the event, summarizing key points and takeaways on the most pressing challenges to developing this emerging class of therapeutics.
Overview of the panel discussion
Panelists included Ansuman Satpathy, MD, PhD, Assistant Professor at the Stanford University School of Medicine; Michael Green, PhD, Director, Translational and Laboratory Research at the University of Texas MD Anderson Cancer Center; and Nick Banovich, PhD, Assistant Professor at Translational Genomics Research Institute. All three researchers are using single cell solutions to study CAR T-cell therapy in various tumors, and in this panel led by Abbey Cutchin, Manager of Oncology Marketing at 10x Genomics, they discussed their insights into the current state of cell and gene therapies for cancer.
The panel discussion was divided into four thematic areas, including characterization of the leukapheresis and infusion product, the evolution of the cell product in vivo, mechanisms of resistance, and next-generation cell therapies. In this recap, we’ll focus mainly on the first two themes, summarizing some of the questions and the panelists’ thought-provoking answers.
Characterization of the leukapheresis and infusion product
Cell therapies are inherently heterogeneous products consisting of different cell types and functional states. Single cell multiomic solutions from 10x Genomics enable researchers to understand how these functional phenotypes contribute to patient variability in response, resistance, and toxicity. With single cell tools, scientists can ask deeper questions, such as, what properties of the apheresis and infusion product contribute to expansion, persistence, and toxicities of cell therapies? How does intrinsic cell product heterogeneity impact efficacy? How does transgene integration site rewire the regulatory profile of engineered cells and impact their functional phenotypes?
What surprised the panelists most when using single cell tools to study the infusion product was the presence of rare cell type populations—accessible only because they were looking at large numbers of cells at increased resolution. In research published in the journal Cell and titled, “Single-cell analyses identify brain mural cells expressing CD19 as potential off-tumor targets for CAR-T immunotherapies,” Dr. Satpathy’s lab showed that, while CD19 was thought to only be expressed by B cells, a rare type of brain cell called mural cells also express the antigen. In a study published in Nature Medicine, “Characteristics of anti-CD19 CAR T cell infusion products associated with efficacy and toxicity in patients with large B cell lymphomas,” Dr. Green’s team discovered a monocyte-like rare cell population that could be associated with the development of immune effector cell-associated neurotoxicity syndrome (ICANS), a severe toxic reaction that some patients develop after infusion. These differences may work synergistically, as in, both intrinsic patient characteristics and variation in the infusion product may drive the development of toxicities or downstream inflammation.
These discoveries—that heterogeneity exists and we now have the tools to study how these cells are being regulated or evolving—are beginning to be incorporated into how cell products are manufactured. “The field is moving from only characterizing what’s happening in an endogenous setting to what’s happening in a manipulated setting, either in CAR T cells or others,” Dr. Satpathy says. All three panelists said that optimizing the selection of cells prior to manufacturing is key to improving a positive response after infusion.
One key issue of this type of therapy is that patients who receive cell therapy have often received multiple lines of treatment prior to being treated with cell therapy. Prior treatment impacts the starting (pre-manufacturing) immune cell population, and immune signatures indicative of a poor response may be visible before a patient is leukapheresed.
“What’s interesting about cellular therapy is that the input material is the culmination of all these other complicated variables before we do the leukapheresis,” Dr. Banovich says. “Clearly whatever’s happening immediately before that in these patients—in our case, patients usually who’ve progressed through multiple lines of treatment for GBM [glioblastoma multiforme] and are really at this last phase of all standard-of-care options—there’s going to be an impact. It’s not clear exactly what those positives and negatives are, but capturing that information will give us insight into how to enrich for those populations in the future.”
Dr. Satpathy thinks there are two sides to this question. “One is, how does prior treatment impact the starting immune population that you put into the pre-manufacturing product, and the second is, how does ongoing combination therapy impact what happens to the product after it goes in, at the level of cell-intrinsic programming of the CAR T cell?” Epigenomic and high-throughput analysis of these cells before and after manufacturing might lend insight into what will work best and be most beneficial for these types of patients.
Evolution of the cell product in vivo
Single cell multiomic approaches are necessary to gain a deeper understanding of how cell therapy behavior changes over time in vivo. 10x Genomics offers single cell solutions to track clonal behavior and kinetics of the infused cells, leading to new insights into underlying clonal phenotypes driving response. With single cell tools, scientists can ask deeper questions, such as, how does the behavior of engineered cells evolve over time in vivo, and, how does cell therapy influence endogenous immune cell populations?
The fact that the cell product does change over time is a given, says Dr. Satpathy, but it’s early days in terms of understanding the changes and opportunities for determining the drivers of these changes. Dr. Banovich is focused on how the cell product impacts or changes the endogenous immune repertoire, and he’s working on developing strategies to do that using Feature Barcode technology to enrich for endogenous or CAR T cells. Panelists agree that determining the best timepoints to measure T-cell activity and proliferation will require longitudinal sample profiling.
Dr. Satpathy and Dr. Banovich performed single cell RNA-sequencing on longitudinal blood samples from patients undergoing cell therapy for different types of tumors. While there are limitations to using blood versus tumor, serial blood samples can be informative of what is potentially going on in the tumor. Dr. Satpathy believes that there is a lot of value in monitoring peripheral blood. His lab has shown that the peripheral immune response to checkpoint immunotherapy is a critical component of that response, as well as more recently that, “a large amount of the effective response comes from peripheral T cells that newly infiltrate the tumor after therapy,” he says. “A large amount of the endogenous T-cell response is present in the peripheral blood, even if it’s at a low frequency—there is gold in peripheral blood to find, in the context of T-cell response.”
“In the GBM clinical trial, we find this robust activation of the endogenous immune system,” Dr. Banovich says, despite cells being delivered directly to the tumor and cerebrospinal fluid through a catheter, including large proliferation of both T cells and myeloid cell components. “A lot of that [immune] signal is also captured in the [pre-treatment] PBMCs [peripheral blood mononuclear cells], so a lot of those same gene expression signals induced in the CSF are also being captured by the PBMCs,” despite the CAR T-cell activity occurring beyond the blood-brain barrier in a distal tissue. This will be useful from a biomarker perspective, he believes.
Dr. Green has used serial blood samples to monitor molecular residual disease and response, which may indicate what’s going on in the tumor. “We would like to monitor change in phenotypes, particularly the relative abundance of different cell populations and how the phenotypes relate to their ability to expand in vivo.” Being able to attain serial biopsies from patients, while a hurdle, is going to help them understand what’s going on in the tumor microenvironment and how that relates to the periphery.
Mechanisms of resistance
Multiple factors contribute to treatment resistance. 10x Genomics offers advanced tools to spatially localize and characterize infused cells in the tumor microenvironment, track immune cell clones, and uncover epigenetic regulators of T-cell exhaustion. With single cell tools, scientists can ask deeper questions, such as, how do immunosuppressive pressures in the tumor microenvironment impact cell therapy infiltration, persistence, and efficacy? What are the epigenetic regulators of exhausted or dysfunctional T-cell phenotypes?
The panel touched briefly on this theme, including what the panelists believe are some of the most pressing challenges in terms of overcoming resistance. “There’s likely very different mechanisms for primary resistance [and] later forms,” Dr. Green says. “The problem will require enormous numbers of samples to capture the diversity of the mechanisms of resistance.”
Dr. Satpathy believes there are at least three primary modes of resistance: CAR T-cell function, tumor-intrinsic escape mechanisms, and the tumor microenvironment. “The good thing is that the field has started to parse these various mechanisms across larger patient cohorts,” he says. “Single cell resolution and functional genomics are critical to understanding those things, now we just have to tackle them one at a time, depending on tumor [type].”
Next-generation cell therapies
One final theme was next-generation therapies. When asked where they see single cell and spatial approaches having the biggest impact in shaping the field in the next five years, all three panelists stressed the power of multiomic analysis.
“There are obvious opportunities to bring cell therapy forward into settings where patients are less pre-treated and have better T cells, so that we can take the fitness of the infusion product out of the equation and focus more on mechanisms of response and resistance,” Dr. Green says. As such, identifying patients who will benefit as well as understanding the role of the tumor microenvironment in these patients will be crucial to making treatment decisions around emerging and traditional therapies.
Dr. Satpathy believes the power of multiomic analysis will continue to shape the field. Over the next five years, he’d like to “bring multiomic, single cell resolution and high-throughput analysis to all these things we’ve talked about,” he says. “Taking these multiomic profiles to understand the molecular programing of a cell is critical.” Now that the field is using different cells—NK, NKT, TReg—“understanding those cell states and what makes a good product is critical.” Secondly, he’d like to bring functional genomics and gene editing into the fold—"how do we edit the critical junctures of what makes a CAR T cell good.” Third, he is excited about using human cell atlases to discover new antigens, de-risk antigens, and identify toxicities.
Finally, getting multiomic kits into the hands of a broader audience will drive the field forward, especially at the intersection of basic and translational science, Dr. Banovich believes. “To make these more broadly adoptable, we have to get these systems more usable in a clinical setting,” he says, which will enable multimodal analysis that goes beyond the bench.
It’s hard not to be excited for the future of cancer immune cell therapies, especially considering the growth of the field and the optimism of those researchers who are already taking advantage of the power of single cell and spatial solutions. We’d like to thank our panel members for their generous contributions to the 10x Genomics Cell and Gene Therapy Symposium and hope you enjoyed the event.
To see the full presentation, watch the roundtable discussion. Visit the 10x Genomics website to learn more about how single cell and spatial solutions are accelerating cancer immune cell therapy research.